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- PDB-5op0: Structure of Prim-PolC from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 5op0
TitleStructure of Prim-PolC from Mycobacterium smegmatis
ComponentsDNA polymerase LigD, polymerase domain
KeywordsTRANSFERASE / Nucleotidyl transferase / Polymerase / Base excision repair
Function / homologyLigD, primase-polymerase domain / DNA ligase D, polymerase domain / metal ion binding / DNA polymerase LigD, polymerase domain
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsBrissett, N.C. / Doherty, A.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J018643/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M004236/1 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: DNA Ligase C and Prim-PolC participate in base excision repair in mycobacteria.
Authors: Pocinski, P. / Brissett, N.C. / Bianchi, J. / Brzostek, A. / Korycka-Machaa, M. / Dziembowski, A. / Dziadek, J. / Doherty, A.J.
History
DepositionAug 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA polymerase LigD, polymerase domain
A: DNA polymerase LigD, polymerase domain


Theoretical massNumber of molelcules
Total (without water)74,4282
Polymers74,4282
Non-polymers00
Water10,269570
1
B: DNA polymerase LigD, polymerase domain


Theoretical massNumber of molelcules
Total (without water)37,2141
Polymers37,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA polymerase LigD, polymerase domain


Theoretical massNumber of molelcules
Total (without water)37,2141
Polymers37,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.550, 56.430, 64.450
Angle α, β, γ (deg.)97.170, 100.200, 90.640
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 7:11 or (resid 12 and (name...
21(chain B and (resseq 7:11 or (resid 12 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRVALVAL(chain A and (resseq 7:11 or (resid 12 and (name...AB7 - 112 - 6
12ASPASPASPASP(chain A and (resseq 7:11 or (resid 12 and (name...AB127
13THRTHRLYSLYS(chain A and (resseq 7:11 or (resid 12 and (name...AB7 - 3362 - 331
14THRTHRLYSLYS(chain A and (resseq 7:11 or (resid 12 and (name...AB7 - 3362 - 331
15THRTHRLYSLYS(chain A and (resseq 7:11 or (resid 12 and (name...AB7 - 3362 - 331
16THRTHRLYSLYS(chain A and (resseq 7:11 or (resid 12 and (name...AB7 - 3362 - 331
17THRTHRLYSLYS(chain A and (resseq 7:11 or (resid 12 and (name...AB7 - 3362 - 331
18THRTHRLYSLYS(chain A and (resseq 7:11 or (resid 12 and (name...AB7 - 3362 - 331
21THRTHRVALVAL(chain B and (resseq 7:11 or (resid 12 and (name...BA7 - 112 - 6
22ASPASPASPASP(chain B and (resseq 7:11 or (resid 12 and (name...BA127
23ALAALALYSLYS(chain B and (resseq 7:11 or (resid 12 and (name...BA6 - 3361 - 331
24ALAALALYSLYS(chain B and (resseq 7:11 or (resid 12 and (name...BA6 - 3361 - 331
25ALAALALYSLYS(chain B and (resseq 7:11 or (resid 12 and (name...BA6 - 3361 - 331
26ALAALALYSLYS(chain B and (resseq 7:11 or (resid 12 and (name...BA6 - 3361 - 331
27ALAALALYSLYS(chain B and (resseq 7:11 or (resid 12 and (name...BA6 - 3361 - 331
28ALAALALYSLYS(chain B and (resseq 7:11 or (resid 12 and (name...BA6 - 3361 - 331

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Components

#1: Protein DNA polymerase LigD, polymerase domain


Mass: 37214.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: ligD, MSMEG_6301 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0R5T1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50mM Tris HCl, 200mM Ammonium Chloride, 10mM Calcium Chloride, 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2015 / Details: KB bimorph mirror pair
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.84→44.771 Å / Num. obs: 110615 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 1.409 % / CC1/2: 0.989 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.119 / Χ2: 0.987 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.84-1.892.60.511.2681590.4930.8695.4
8.23-44.772.90.03811.412920.990.06696.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.01 Å44.77 Å
Translation4.01 Å44.77 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.6.1phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IRY

2iry


Resolution: 1.84→44.771 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.64
RfactorNum. reflection% reflection
Rfree0.2092 2941 4.94 %
Rwork0.1858 --
obs0.187 59594 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.74 Å2 / Biso mean: 29.6374 Å2 / Biso min: 10.4 Å2
Refinement stepCycle: final / Resolution: 1.84→44.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 0 570 5801
Biso mean---37.11 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055401
X-RAY DIFFRACTIONf_angle_d0.7437376
X-RAY DIFFRACTIONf_chiral_restr0.047797
X-RAY DIFFRACTIONf_plane_restr0.006981
X-RAY DIFFRACTIONf_dihedral_angle_d16.2273294
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2999X-RAY DIFFRACTION6.019TORSIONAL
12B2999X-RAY DIFFRACTION6.019TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.87020.30081220.25452668279095
1.8702-1.90240.30871400.25112680282096
1.9024-1.9370.29441340.23422633276795
1.937-1.97430.26451340.23512686282095
1.9743-2.01460.28171630.24792642280595
2.0146-2.05840.25971610.22772637279897
2.0584-2.10630.28711440.21382680282497
2.1063-2.15890.23611340.19642733286797
2.1589-2.21730.2241480.19652671281997
2.2173-2.28260.21371260.18662698282497
2.2826-2.35620.2441470.19392736288398
2.3562-2.44040.23691270.19872708283597
2.4404-2.53810.221380.20252716285497
2.5381-2.65360.23171400.19722713285398
2.6536-2.79350.20661350.19472742287798
2.7935-2.96850.22451490.19122731288098
2.9685-3.19770.21411280.18722748287698
3.1977-3.51930.20691470.18242696284397
3.5193-4.02830.17011410.16152721286297
4.0283-5.07410.17031390.14952701284097
5.0741-44.78380.1531440.16572713285798

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